Name: Holdemania filiformis DSM 12042
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5373

Type strain:

Species: Holdemania filiformis

Culture col. no.: DSM 12042, ATCC 51649, CCUG 39501, VPI J1-31B-1

Strain history: <- ATCC <- L.V. Moore, VPI J1-31B-1 <- W.E.C. Moore (Eubacterium sp.)

NCBI tax ID(s): 545696 (strain), 61171 (species)

SI-ID 45309

ATCC 51649, CCUG 39501, DSM 12042

Special Collections

DSMZ
CCUG

Section

Holdemania filiformis DSM 12042 is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from human feces.

Gram-positive
spore-forming
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Erysipelotrichaceae*
	Genus	*Holdemania*
	Species	**Holdemania filiformis**
	Full Scientific Name (LPSN)	Holdemania filiformis Willems et al. 1997

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4586]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #4586]

Culture medium growth

[Ref.: #4586]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4586]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4586]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4586]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %92

[Ref.: #4586]	Murein short key	B13
[Ref.: #4586]	Murein types	B1delta {L-Ser} [L-Ala] D-Glu-L-Asp-L-Lys

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	+	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	+		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	+		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #4586]	12592	-	-	-	+	-	+/-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+	+	-	-	-	+	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	peptidoglycan biosynthesis	93.33	14 of 15
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	glutamate and glutamine metabolism	57.14	16 of 28
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	flavin biosynthesis	53.33	8 of 15
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	lysine metabolism	38.1	16 of 42
[Ref.: #66794]	isoleucine metabolism	37.5	3 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	tryptophan metabolism	36.84	14 of 38
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	histidine metabolism	31.03	9 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	leucine metabolism	23.08	3 of 13
[Ref.: #66794]	urea cycle	23.08	3 of 13
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	CO2 fixation in Crenarchaeota	22.22	2 of 9
[Ref.: #66794]	cysteine metabolism	22.22	4 of 18
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4586]	Sample type/isolated from	human feces
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y11466 (>99% sequence identity) for Holdemania filiformis from Microbeatlas

Aquatic Samples	486
Soil Samples	49
Animal Samples	34370
Plant Samples	14
Total Samples	34919

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4586]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4586]	H.filiformis 16S rRNA gene	Y11466	1391	GenBank ENA	61171 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Holdemania filiformis DSM 12042	GCA_000157995	scaffold	GenBank ENA	545696 tax ID	*
[Ref.: #66792]	Holdemania filiformis DSM 12042	545696.5	wgs	PATRIC	545696 tax ID	*
[Ref.: #66792]	Holdemania filiformis VPI J1-31B-1, DSM 12042	643886103	draft	JGI IMG/M	545696 tax ID	*

[Ref.: #4586]

GC-content

38 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Holdemania filiformis DSM 12042 PATRIC: 545696.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	92	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Holdemania filiformis DSM 12042 DSM 12042 NCBI: GCA_000157995.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	67.675	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	84.785	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	94.104	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	60.319	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.772	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	85.131	no

Availability in culture collections External links

[Ref.: #4586]

Culture collection no.

DSM 12042, ATCC 51649, CCUG 39501, VPI J1-31B-1

[Ref.: #74863]

SI-ID 45309

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phenotypic and phylogenetic characterization of some Eubacterium-like isolates containing a novel type B wall murein from human feces: description of Holdemania filiformis gen. nov., sp. nov.	Willems A, Moore WE, Weiss N, Collins MD	Int J Syst Bacteriol	10.1099/00207713-47-4-1201	1997	*

References

#4586

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12042

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#68380

Automatically annotated from API rID32A .

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#74863

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID45309.1 )

* These data were automatically processed and therefore are not curated

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Holdemania filiformis DSM 12042

Holdemania filiformis DSM 12042 DSM 12042

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